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Official Description

Molecular cytogenetics; DNA probe, each (eg, FISH)

© Copyright 2026 American Medical Association. All rights reserved.

Common Language Description

The CPT® Code 88271 refers to a laboratory test that focuses on molecular cytogenetics, specifically utilizing DNA probes such as fluorescence in situ hybridization (FISH). This procedure is essential for analyzing the genetic material found in various biological samples, including bone marrow, whole blood, amniotic fluid, or chorionic villi. Molecular cytogenetics is a branch of genetics that studies the structure and function of chromosomes, including their abnormalities and variations. The insights gained from these studies are crucial for understanding various genetic conditions and diseases. The samples required for this test are typically obtained through specific procedures like venipuncture, bone marrow aspiration, amniocentesis, or chorionic villus sampling, which are separately reportable. The test is particularly valuable for rapid detection of aneuploidy in chromosomes X, Y, 13, 18, and 21, which can indicate certain genetic disorders. Additionally, it plays a significant role in the risk stratification of conditions such as multiple myeloma, the detection of genomic abnormalities in chronic lymphocytic leukemia, and the diagnosis of acute lymphocytic leukemia. Furthermore, it aids in distinguishing between aggressive lymphomas and monitoring minimal residual disease in patients with therapy-related myelodysplastic syndrome or acute myelogenous leukemia. The examination of whole blood can also help identify chromosome deletions or duplications in individuals with a family history of genetic defects, and it is instrumental in excluding specific genetic rearrangements in patients with various forms of leukemia.

© Copyright 2026 Coding Ahead. All rights reserved.

1. Indications

The procedure associated with CPT® Code 88271 is indicated for a variety of clinical scenarios where molecular cytogenetic analysis is necessary. The following conditions and situations warrant the use of this test:

  • Detection of Aneuploidy Rapid detection of aneuploidy in chromosomes X, Y, 13, 18, and 21, particularly in maternal amniotic fluid or chorionic villi and whole blood in infants.
  • Multiple Myeloma Risk Stratification Examination of bone marrow or whole blood to assess risk stratification in individuals diagnosed with multiple myeloma.
  • Chronic Lymphocytic Leukemia Identification of important genomic abnormalities in patients with chronic lymphocytic leukemia.
  • Eosinophilia and Hematopoietic Neoplasms Aid in the diagnosis and classification of eosinophilia presenting hematopoietic neoplasms.
  • Acute Lymphocytic Leukemia Support the diagnosis of acute lymphocytic leukemia through genetic analysis.
  • Lymphoma Differentiation Assist in diagnosing and predicting aggressive morphologic features or distinguishing between Burkitt lymphoma and diffuse large B-cell lymphoma.
  • Minimal Residual Disease Monitoring Diagnose, predict, or monitor minimal residual disease in therapy-related myelodysplastic syndrome (MDS) or acute myelogenous leukemia associated with MDS.
  • Genetic Defect Identification Detect or identify chromosome deletion or duplication in individuals with a family history of genetic defects.
  • Exclusion of Genetic Rearrangements Exclude cryptic BCR-ABL1 rearrangement in patients with myelogenous leukemia or PDGFRA abnormality in patients with neoplastic eosinophilia, and confirm PML-RARA translocation for acute promyelocytic leukemia.

2. Procedure

The procedure for CPT® Code 88271 involves several critical steps to ensure accurate molecular cytogenetic analysis. Each step is designed to facilitate the collection and examination of genetic material from the specified biological samples.

  • Sample Collection The first step involves obtaining the necessary biological samples, which may include bone marrow, whole blood, amniotic fluid, or chorionic villi. These samples are collected through procedures such as venipuncture for blood, bone marrow aspiration for marrow samples, amniocentesis for amniotic fluid, or chorionic villus sampling for chorionic villi. Each of these collection methods is performed under sterile conditions to prevent contamination and ensure the integrity of the samples.
  • Preparation of Samples Once collected, the samples are prepared for analysis. This preparation may involve processing the samples to isolate the DNA and ensure that it is suitable for hybridization. The samples are treated with specific reagents that facilitate the binding of DNA probes to the target sequences within the chromosomes.
  • Fluorescence In Situ Hybridization (FISH) The core of the procedure is the application of fluorescence in situ hybridization (FISH). This technique involves applying fluorescently labeled DNA probes to the prepared samples. These probes are designed to bind to specific regions of the chromosomes, allowing for the visualization of genetic material under a fluorescence microscope. The binding of the probes indicates the presence or absence of specific chromosomal abnormalities.
  • Analysis of Results After the FISH procedure, the samples are analyzed to identify any chromosomal abnormalities. This analysis is performed by trained laboratory personnel who interpret the fluorescence signals to determine the presence of aneuploidy, deletions, duplications, or other genetic rearrangements. The results are documented and reported to the referring physician for further clinical decision-making.

3. Post-Procedure

Post-procedure care for patients undergoing testing associated with CPT® Code 88271 typically involves monitoring for any immediate complications related to the sample collection methods, such as venipuncture or bone marrow aspiration. Patients may experience mild discomfort or bruising at the site of the procedure, which usually resolves without intervention. The results of the molecular cytogenetic analysis are generally available within a specified timeframe, depending on the laboratory's processing capabilities. Physicians will review the findings to guide further diagnostic or therapeutic decisions based on the identified genetic abnormalities. It is essential for healthcare providers to communicate the results to patients and discuss any necessary follow-up actions or additional testing that may be required based on the findings.

Short Descr CYTOGENETICS DNA PROBE
Medium Descr MOLECULAR CYTOGENETICS DNA PROBE EACH
Long Descr Molecular cytogenetics; DNA probe, each (eg, FISH)
Status Code Statutory Exclusion (from MPFS, may be paid under other methodologies)
Global Days XXX - Global Concept Does Not Apply
PC/TC Indicator (26, TC) 9 - Not Applicable
Multiple Procedures (51) 9 - Concept does not apply.
Bilateral Surgery (50) 9 - Concept does not apply.
Physician Supervisions 09 - Concept does not apply.
Assistant Surgeon (80, 82) 9 - Concept does not apply.
Co-Surgeons (62) 9 - Concept does not apply.
Team Surgery (66) 9 - Concept does not apply.
Diagnostic Imaging Family 99 - Concept Does Not Apply
CLIA Waived (QW) No
APC Status Indicator Conditionally packaged laboratory tests
Type of Service (TOS) 5 - Diagnostic Laboratory
Berenson-Eggers TOS (BETOS) T1H - Lab tests - other (non-Medicare fee schedule)
MUE 16
CCS Clinical Classification 235 - Other Laboratory
90 Reference (outside) laboratory: when laboratory procedures are performed by a party other than the treating or reporting physician or other qualified health care professional, the procedure may be identified by adding modifier 90 to the usual procedure number.
59 Distinct procedural service: under certain circumstances, it may be necessary to indicate that a procedure or service was distinct or independent from other non-e/m services performed on the same day. modifier 59 is used to identify procedures/services, other than e/m services, that are not normally reported together, but are appropriate under the circumstances. documentation must support a different session, different procedure or surgery, different site or organ system, separate incision/excision, separate lesion, or separate injury (or area of injury in extensive injuries) not ordinarily encountered or performed on the same day by the same individual. however, when another already established modifier is appropriate it should be used rather than modifier 59. only if no more descriptive modifier is available, and the use of modifier 59 best explains the circumstances, should modifier 59 be used. note: modifier 59 should not be appended to an e/m service. to report a separate and distinct e/m service with a non-e/m service performed on the same date, see modifier 25.
91 Repeat clinical diagnostic laboratory test: in the course of treatment of the patient, it may be necessary to repeat the same laboratory test on the same day to obtain subsequent (multiple) test results. under these circumstances, the laboratory test performed can be identified by its usual procedure number and the addition of modifier 91. note: this modifier may not be used when tests are rerun to confirm initial results; due to testing problems with specimens or equipment; or for any other reason when a normal, one-time, reportable result is all that is required. this modifier may not be used when other code(s) describe a series of test results (eg, glucose tolerance tests, evocative/suppression testing). this modifier may only be used for laboratory test(s) performed more than once on the same day on the same patient.
GZ Item or service expected to be denied as not reasonable and necessary
GA Waiver of liability statement issued as required by payer policy, individual case
XU Unusual non-overlapping service, the use of a service that is distinct because it does not overlap usual components of the main service
Q1 Routine clinical service provided in a clinical research study that is in an approved clinical research study
76 Repeat procedure or service by same physician or other qualified health care professional: it may be necessary to indicate that a procedure or service was repeated by the same physician or other qualified health care professional subsequent to the original procedure or service. this circumstance may be reported by adding modifier 76 to the repeated procedure or service. note: this modifier should not be appended to an e/m service.
XP Separate practitioner, a service that is distinct because it was performed by a different practitioner
TC Technical component; under certain circumstances, a charge may be made for the technical component alone; under those circumstances the technical component charge is identified by adding modifier 'tc' to the usual procedure number; technical component charges are institutional charges and not billed separately by physicians; however, portable x-ray suppliers only bill for technical component and should utilize modifier tc; the charge data from portable x-ray suppliers will then be used to build customary and prevailing profiles
GC This service has been performed in part by a resident under the direction of a teaching physician
GY Item or service statutorily excluded, does not meet the definition of any medicare benefit or, for non-medicare insurers, is not a contract benefit
XS Separate structure, a service that is distinct because it was performed on a separate organ/structure
26 Professional component: certain procedures are a combination of a physician or other qualified health care professional component and a technical component. when the physician or other qualified health care professional component is reported separately, the service may be identified by adding modifier 26 to the usual procedure number.
58 Staged or related procedure or service by the same physician or other qualified health care professional during the postoperative period: it may be necessary to indicate that the performance of a procedure or service during the postoperative period was: (a) planned or anticipated (staged); (b) more extensive than the original procedure; or (c) for therapy following a surgical procedure. this circumstance may be reported by adding modifier 58 to the staged or related procedure. note: for treatment of a problem that requires a return to the operating/procedure room (eg, unanticipated clinical condition), see modifier 78.
AQ Physician providing a service in an unlisted health professional shortage area (hpsa)
GW Service not related to the hospice patient's terminal condition
XE Separate encounter, a service that is distinct because it occurred during a separate encounter
Date
Action
Notes
2017-01-01 Changed Guideline added.
2011-01-01 Changed Short description changed.
1999-01-01 Added First appearance in code book in 1999.
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